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oneliners

Useful bash one-liners for bioinformatics.

outrigger

Create a *de novo* alternative splicing database, validate splicing events, and quantify percent spliced-in (Psi) from RNA seq data

paga

Mapping topologies of complex manifolds.

pairwise-discreteness-testing

patchwork

The Composer of ggplots

phate

PHATE (Potential of Heat-diffusion for Affinity-based Transition Embedding) is a tool for visualizing high dimensional single cell data with natural progressions or trajectories.

phenograph

Subpopulation detection in high-dimensional single-cell data

pycon2014_dataviz

Computational data visualization. Presented at PyCon 2014 lightning talks.

pyscenic

pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.

pyscuba

Python for Single-cell Clustering Using Bifurcation Analysis

python-100-days

Python - 100天从新手到大师

qtcat

Quantitative Trait Cluster Association Test in R

rca

Residual Component Analysis

rca-1

R package for robust clustering of single cell RNA sequencing data

reticulate

R Interface to Python

rforbioinformatics

rna-seq-analysis

RNAseq analysis notes from Ming Tang

rnaseek

Scripts and modules for parsing and aggregating output files from RNA-sequencing data

rnaseqlib

RNA-Seq pipeline

robust-pca

A simple Python implementation of R-PCA

rosalind

learning bioinformatics and programming through problem solving.

rsnps

Wrapper to a number of SNP web APIs

saver

Single-cell RNA-seq Gene Expression Recovery

scanalysistutorial

scanpy

Single-Cell Analysis in Python. Scales to >1M cells.

scenic

SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.

scgps

A framework for clustering (CORE) and estimation of relationship between pairs of clusters (scGPS) from single cell data

scode

SCODE : an efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation

scrna-seq_10x

10X 单细胞册数数据分析手册

scrna-seq_notes

A list of scRNA-seq analysis tools